BacDive transformer opens ncbitaxon.owl with a sqlite adapter (path/format mismatch)

[turbomam]

Symptom

BacDive transformer fails when opening the NCBI taxonomy resource — get_adapter is called with sqlite:…ncbitaxon.owl.

Cause

# constants.py
NCBITAXON_SOURCE = RAW_DATA_DIR / "ncbitaxon.owl"

# kg_microbe/transform_utils/bacdive/bacdive.py
self.ncbi_impl = get_adapter(f"sqlite:{NCBITAXON_SOURCE}")  # sqlite: + .owl — wrong

The sqlite adapter expects a .db file; the ncbitaxon.db needed here exists under data/raw/ (built via semsql from the OWL).

Recommended fix

self.ncbi_impl = get_adapter(f"sqlite:{RAW_DATA_DIR}/ncbitaxon.db")

Single-line change in the BacDive transformer. Aligns with the already-built local ncbitaxon.db.

Alternative: add a Makefile rule to build `ncbitaxon.db` from `ncbitaxon.owl` via semsql/runoak

Shape: data/raw/ncbitaxon.db: data/raw/ncbitaxon.owl. Generalizes for fresh clones that don't already have the DB built. More work; value depends on whether the DB is typically pre-provisioned.

Alternative: split into separate OWL and DB constants in constants.py

Reduces ambiguity but requires updating all callsites that use NCBITAXON_SOURCE.